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Job request: 384

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-thrombosis
ID:
wj7eu6yscepptoc5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Walker requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    000_covid
    Status:
    Status: Succeeded
    Job identifier:
    ltyhw62guaxbmdhw
  • Action:
    000_pneumonia
    Status:
    Status: Succeeded
    Job identifier:
    kkvfwi3f7oqziwne
  • Action:
    matching_data_management
    Status:
    Status: Failed
    Job identifier:
    o5gzlakxjx3riszo
    Error:
    Job exited with an error code
  • Action:
    302_pneumonia
    Status:
    Status: Failed
    Job identifier:
    nvk3tdolt3fqof2v
    Error:
    Not starting as dependency failed
  • Action:
    302_control_2020
    Status:
    Status: Failed
    Job identifier:
    znkxd7buf5253aaz
    Error:
    Not starting as dependency failed
  • Action:
    302_control_2019
    Status:
    Status: Failed
    Job identifier:
    imk63ddwkwuu46ut
    Error:
    Not starting as dependency failed
  • Action:
    301_control_2019
    Status:
    Status: Failed
    Job identifier:
    44xndcx5qp4bvx46
    Error:
    Not starting as dependency failed
  • Action:
    301_control_2020
    Status:
    Status: Failed
    Job identifier:
    rcgrt65otayoojym
    Error:
    Not starting as dependency failed
  • Action:
    301_pneumonia
    Status:
    Status: Failed
    Job identifier:
    qrmn7ifpvrsi7enx
    Error:
    Not starting as dependency failed
  • Action:
    201_covid
    Status:
    Status: Succeeded
    Job identifier:
    chpv3s3a63olaqkt
  • Action:
    201_pneumonia
    Status:
    Status: Succeeded
    Job identifier:
    43iwru6w4ulyv4jn

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_cohorts:
    run: cohortextractor:latest generate_cohort
    outputs:
      highly_sensitive:
        covid_cohort: output/input_covid.csv
        pneumonia_cohort: output/input_pneumonia.csv
        ctrl_2019_cohort: output/input_control_2019.csv
        ctrl_2020_cohort: output/input_control_2020.csv

  000_covid:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_covid.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta

  000_pneumonia:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_pneumonia.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta

  201_covid:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [000_covid]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_covid.csv

  201_pneumonia:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [000_pneumonia]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_pneumonia.csv

  matching_control_2019:
    run: python:latest python analysis/match_running.py "control_2019"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2019.txt
      highly_sensitive:
        combined: output/matched_combined_control_2019.csv

  matching_control_2020:
    run: python:latest python analysis/match_running.py "control_2020"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2020.txt
      highly_sensitive:
        combined: output/matched_combined_control_2020.csv

  matching_data_management:
    run: stata-mp:latest analysis/300_cr_data_management_matching.do 
    needs: [generate_cohorts, matching_control_2019, matching_control_2020]
    outputs:
      highly_sensitive:
        combined3: output/matched_combined_pneumonia.dta
        combined4: output/matched_combined_control_2019.dta
        combined5: output/matched_combined_control_2020.dta

  301_pneumonia:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "pneumonia"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_pneumonia.dta

  301_control_2019:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2019"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_control_2019.dta

  301_control_2020:
    run: stata-mp:latest analysis/301_cr_define_covariates_matched_groups.do "control_2020"
    needs: [matching_data_management]
    outputs:
      highly_sensitive:
        combined1: output/matched_cohort_control_2020.dta

  302_pneumonia:
    run: stata-mp:latest analysis/302_cox_models.do "pneumonia"
    needs: [301_pneumonia]
    outputs:
      moderately_sensitive:
        combined1: output/tabfig/cox_model_summary_pneumonia.csv

  302_control_2019:
    run: stata-mp:latest analysis/302_cox_models.do "control_2019"
    needs: [301_control_2019]
    outputs:
      moderately_sensitive:
        combined1: output/tabfig/cox_model_summary_control_2019.csv

  302_control_2020:
    run: stata-mp:latest analysis/302_cox_models.do "control_2020"
    needs: [301_control_2020]
    outputs:
      moderately_sensitive:
        combined1: output/tabfig/cox_model_summary_control_2020.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:17

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-thrombosis
Requested by
Alex Walker
Branch
master
Force run dependencies
No
Git commit hash
da065af
Requested actions
  • 000_covid
  • 000_pneumonia
  • 201_covid
  • 201_pneumonia
  • matching_data_management
  • 301_pneumonia
  • 301_control_2019
  • 301_control_2020
  • 302_pneumonia
  • 302_control_2019
  • 302_control_2020

Code comparison

Compare the code used in this job request